44 Works

Bacillus subtilis YolD protein

The YolD family (that includes both Bacillus subtilis YolD (this model) and YqjX) is part of the WYL-like superfamily, predicted to have an SH3 β-barrel fold related to Sm domains. In our analysis, among the closest detected structural matches were E. coli YaeO, a Rho-specific inhibitor of transcription termination, and a cyanobacterial Hfq homolog. Model assessment showed that YqjX and YolD sequences are indeed compatible with the SH3 β-barrel structure. Interestingly, UmuD' has an all...

Sulprostone docked Human Prostanoid E2 Receptor Subtype 4 (hEP4)

The EP4 prostanoid receptor is one of four GPCRs that mediate the diverse actions of prostaglandin E2 (PGE2). Novel selective EP4 receptor agonists would assist to further elucidate receptor sub-type function and promote development of therapeutics for bone healing, heart failure, and other receptor associated conditions. Homology models were generated by threading for human and rat EP4 receptors using the RaptorX server. These models were fit to an implicit membrane using the PPM server and...

11-deoxy-PGE1 docked Human Prostanoid E2 Receptor Subtype 4 (hEP4)

The EP4 prostanoid receptor is one of four GPCRs that mediate the diverse actions of prostaglandin E2 (PGE2). Novel selective EP4 receptor agonists would assist to further elucidate receptor sub-type function and promote development of therapeutics for bone healing, heart failure, and other receptor associated conditions. Homology models were generated by threading for rat and human EP4 receptors using the RaptorX server. These models were fit to an implicit membrane using the PPM server and...

Structural determination of hexose transporter Plasmodium falciparum (PfHT) by homology modeling

Malaria is the most prevalent parasitic disease in the world. Currently, an effective vaccine for malaria does not exist, and chemotherapy must be used to treat the disease. Because of increasing resistance to current antimalarial drugs, new treatments must be developed. Among the many potential molecular targets, the hexose transporter of Plasmodium falciparum (PfHT) is particularly promising because it plays a vital role in glucose transport for the parasite. Thus, this study aims to determine...

C-terminal domain of Mycobacterium tuberculosis polymerase DinX

The C-terminal extension of Mycobacterium tuberculosis DinX Y-family polymerase features a Tudor-like domain, the closest structural homolog being the RNA polymerase interacting domain at the C-terminus of PcrA/UvrD helicase. Similarly to the C-terminal domain of PcrA/UvrD helicase, the DinX may also interact with the RNA polymerase and play a role in transcription-coupled DNA repair.

Complex of Escherichia coli RecA and UmuC-CT motif

Many Y-family polymerases, including Escherichia coli UmuC (featured in this model), have a RecA-NT-like motif in their C-terminal extensions. Through this motif, they can form a complex with RecA, very similar to the RecA-NT-RecA complex.

Structural characterization of an Arf dimer interface: molecular mechanism of Arf-dependent membrane scission

The aim of the work was to model the homodimer of Arf1. Interaction interfaces were predicted using the web servers PINTS and meta-PPISP. The dimer was predicted by rigid-body docking using ClusPro. The model obtained agrees with experimental data from hydrogen exchange mass spectrometry.

3D model of SARS-CoV-2 NSP14-NSP10 hetero-oligomeric complex for pocket mapping

We have generated a 3D structure of the SARS-CoV-2 NSP14-NSP10 hetero-oligomeric complex. The structure model has been used for the exploration of the potential binding cavities within promising Covid-19 proteins. After in silico modelling of these 3D structures, such a mapping enables the identification of the most relevant binding sites for which virtual screening simulations or de novo rational design should allow the identification of promising hits. This study provides a novel strategy for pocket...

Mycoplasma pneumoniae ribosome in PUM-stalled expressome

Structural biology performed inside cells can capture molecular machines in action within their native context. Here we developed an integrative in-cell structural approach using the genome-reduced human pathogen Mycoplasma pneumoniae. We combined whole-cell crosslinking mass spectrometry, cellular cryo-electron tomography, and integrative modeling to determine an in-cell architecture of a transcribing and translating expressome at sub-nanometer resolution. The expressome comprises RNA polymerase (RNAP), the ribosome, and the transcription elongation factors NusG and NusA. We pinpointed NusA...

COMPUTATIONAL MODEL STRUCTURE OF SARS-CoV-2 NON-STRUCTURAL PROTEIN 9b

The structure of 'SARS-CoV-2 nonstructural protein 9b” is a part of the project “Sequence analysis and structure prediction of SARS-CoV-2 accessory proteins 9b and ORF14: evolutionary analysis indicates close relatedness to bat coronavirus” (Baruah et al., 2020; ChemRxiv. Preprint. https://doi.org/10.26434/chemrxiv.12424958.v1) based on the sequence analysis and complete coordinate structure prediction of UniProtkB reviewed sequence data.

Assembled fragment compound targeting pre-miR-21

Small molecule fragments containing photoreactive diazirine moieties were screened for binding to the oncogenic non-coding microRNA precursor to miR-21 (pre-miR-21). By assembling a fragment and RNA binding module previously identified, a bioactive ligand was discovered that modulated miR-21 biology in cells. The compound selectively affects an invasive phenotype for triple negative breast cancer cells that is mediated by miR-21 over expression. The de novo model of the compound interacting with the Dicer processing site of...

Hypothetical model of Dual Oxidase

The present study focused on theoretical modeling of dual oxidase (UniProt Id: Q9VQH2) of Drosophila melanogaster by comparative homology modeling. It plays an important role in innate immunity limiting microbial proliferation in the gut and acts downstream of a hh-signaling pathway to induce the production of reactive oxygen species (ROS) in response to intestinal bacterial infection. It may also generate antimicrobial oxidative burst through its peroxidase-like domain (UniPrort annotated data). The model is further energy...

PcC7758

Juveniles of the leaf beetle Phaedon cochleariae synthesize iridoid via the mevalonate pathway for repelling predators. The entry from regular terpenoid biosynthesis into the dedicated defensive pathway is achieved by ω-hydroxylation of geraniol to 8-hydroxygeraniol. Here we describe the identification and characterization of the geraniol 8-hydroxylase as a P450 monooxygenase using integrated transcriptomics and proteomics analysis. In the fat body, 73 individual cytochrome P450s were identified. Double stranded RNA (dsRNA)-mediated knock down of CYP6BH5 led...

Mycoplasma pneumoniae chloramphenicol-bound ribosome

Structural biology performed inside cells can capture molecular machines in action within their native context. Here we developed an integrative in-cell structural approach using the genome-reduced human pathogen Mycoplasma pneumoniae. We combined whole-cell crosslinking mass spectrometry, cellular cryo-electron tomography, and integrative modeling to determine an in-cell architecture of a transcribing and translating expressome at sub-nanometer resolution. The expressome comprises RNA polymerase (RNAP), the ribosome, and the transcription elongation factors NusG and NusA. We pinpointed NusA...

Homology model of RhlR

RhlR protein is a transcription regulator of the hcnABC operon of opportunistic human pathogen Pseudomonas aeruginosa. The protein is a DNA binding protein and binds to the promoter DNA as a dimer. However, the structural details of the RhlR protein is not available. Therefore, we tried to predict the three dimensional structure of the RhlR protein by homology modelling. We also tried to identify the binding interactions of the protein with the promoter DNA region.

Equine Prolactin Receptor

In case of horse breeding, prolactin can have a particular influence once equines are known for presenting several reproductive disorders. Single nucleotide polymorphisms are the main type of mutation found, and were already described in coding regions of equine prolactin hormone and receptor. Without any complete model, in silico studies using several bioinformatics analysis were performed, aiming to contribute in the elucidation of structural and functional aspects related to this protein. We provide the first...

PGE2 docked Human Prostanoid E2 Receptor Subtype 4 (hEP4)

The EP4 prostanoid receptor is one of four GPCRs that mediate the diverse actions of prostaglandin E2 (PGE2). Novel selective EP4 receptor agonists would assist to further elucidate receptor sub-type function and promote development of therapeutics for bone healing, heart failure, and other receptor associated conditions. Homology models were generated by threading for human and rat EP4 receptors using the RaptorX server. These models were fit to an implicit membrane using the PPM server and...

PGE2 docked Rat Prostanoid E2 Receptor Subtype 4 (rEP4)

The EP4 prostanoid receptor is one of four GPCRs that mediate the diverse actions of prostaglandin E2 (PGE2). Novel selective EP4 receptor agonists would assist to further elucidate receptor sub-type function and promote development of therapeutics for bone healing, heart failure, and other receptor associated conditions. Homology models were generated by threading for human and rat EP4 receptors using the RaptorX server. These models were fit to an implicit membrane using the PPM server and...

Equine Prolactin

In case of horse breeding, prolactin can have a particular influence once equines are known for presenting several reproductive disorders. Single nucleotide polymorphisms are the main type of mutation found, and were already described in coding regions of equine prolactin hormone and receptor. Without any complete model, in silico studies using several bioinformatics analysis were performed, aiming to contribute in the elucidation of structural and functional aspects related to this protein. We provide the first...

Registration Year

  • 2020
    44

Resource Types

  • Model
    44